Strain identifier

BacDive ID: 5479

Type strain: Yes

Species: Aequorivita capsosiphonis

Strain Designation: A71

Strain history: <- CN Seong, Sunchon Natl. Univ.

NCBI tax ID(s): 1120951 (strain), 487317 (species)

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General

@ref: 17398

BacDive-ID: 5479

DSM-Number: 23843

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Aequorivita capsosiphonis A71 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

NCBI tax idMatching level
487317species
1120951strain

strain history

@refhistory
17398<- KCTC <- C. N. Seong, Sunchon Natl. Univ., Korea
67770C. N. Seong A71.
67771<- CN Seong, Sunchon Natl. Univ.

doi: 10.13145/bacdive5479.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aequorivita
  • species: Aequorivita capsosiphonis
  • full scientific name: Aequorivita capsosiphonis Park et al. 2009

@ref: 17398

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aequorivita

species: Aequorivita capsosiphonis

full scientific name: Aequorivita capsosiphonis Park et al. 2009 emend. Liu et al. 2013

strain designation: A71

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29016negative2.5 µm0.35 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.975

pigmentation

  • @ref: 29016
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17398
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17398positivegrowth25mesophilic
29016positivegrowth04-40
29016positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29016positivegrowth07-09alkaliphile
29016positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29016aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.984

halophily

  • @ref: 29016
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <10 %

observation

  • @ref: 29016
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2901615963ribitol+carbon source
2901622653asparagine+carbon source
2901635391aspartate+carbon source
2901616947citrate+carbon source
2901633984fucose+carbon source
2901624148galactonate+carbon source
290165291gelatin+carbon source
2901628087glycogen+carbon source
2901617596inosine+carbon source
2901617716lactose+carbon source
2901615792malonate+carbon source
2901617272propionate+carbon source
2901616634raffinose+carbon source
2901630911sorbitol+carbon source
2901617992sucrose+carbon source
2901626986threonine+carbon source
2901616704uridine+carbon source

enzymes

@refvalueactivityec
29016acid phosphatase+3.1.3.2
29016alkaline phosphatase+3.1.3.1
29016catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17398seawaterSouth Sea, Gwangyang BayRepublic of KoreaKORAsia
67770Green alga Capsosiphon fulvescensRepublic of KoreaKORAsiaCapsosiphon fulvescens
67771From seawaterGwangyang BayRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_259.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_74;96_182;97_198;98_221;99_259&stattab=map
  • Last taxonomy: Aequorivita capsosiphonis subclade
  • 16S sequence: EU290153
  • Sequence Identity:
  • Total samples: 1186
  • soil counts: 150
  • aquatic counts: 361
  • animal counts: 649
  • plant counts: 26

Safety information

risk assessment

  • @ref: 17398
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17398
  • description: Aequorivita capsosiphonis strain A71 16S ribosomal RNA gene, partial sequence
  • accession: EU290153
  • length: 1412
  • database: ena
  • NCBI tax ID: 487317

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aequorivita capsosiphonis DSM 238431120951.3wgspatric1120951
66792Aequorivita capsosiphonis DSM 238432524023070draftimg1120951
67770Aequorivita capsosiphonis DSM 23843GCA_000429125scaffoldncbi1120951

GC content

@refGC-contentmethod
2901636.9
6777036.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.703no
flagellatedno95.258no
gram-positiveno97.657yes
anaerobicno99.378yes
aerobicyes86.504no
halophileyes73.103yes
spore-formingno94.445no
thermophileno99.626yes
glucose-utilyes80.256no
glucose-fermentno91.307no

External links

@ref: 17398

culture collection no.: DSM 23843, JCM 15070, KCTC 22183

straininfo link

  • @ref: 74966
  • straininfo: 399313

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329596Aequorivita capsosiphonis sp. nov., isolated from the green alga Capsosiphon fulvescens, and emended description of the genus Aequorivita.Park SC, Baik KS, Kim MS, Kim SS, Kim SR, Oh MJ, Kim D, Bang BH, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.004119-02009Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny23435250Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis.Liu JJ, Zhang XQ, Pan J, Sun C, Zhang Y, Li CQ, Zhu XF, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.049635-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Glycolipids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17398Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23843)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23843
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29016Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2544628776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74966Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399313.1StrainInfo: A central database for resolving microbial strain identifiers